This invention provides methods of monitoring the expression levels of a multiplicity
of genes. The methods involve hybridizing a nucleic acid sample to a high density
array of oligonucleotide probes where the high density array contains oligonucleotide
probes complementary to subsequences of target nucleic acids in the nucleic acid
sample. In one embodiment, the method involves providing a pool of target nucleic
acids comprising RNA transcripts of one or more target genes, or nucleic acids
derived from the RNA transcripts, hybridizing said pool of nucleic acids to an
array of oligonucleotide probes immobilized on surface, where the array comprising
more than 100 different oligonucleotides and each different oligonucleotide is
localized in a predetermined region of the surface, the density of the different
oligonucleotides is greater than about 60 different oligonucleotides per 1 cm2,
and the olignucleotide probes are complementary to the RNA transcripts or nucleic
acids derived from the RNA transcripts; and quantifying the hybridized nucleic
acids in the array.
